Contacts of the strand formed by residues 54 - 60 (chain A) in PDB entry 1K4R
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ALA 54 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A GLN* 4.7 2.2 - - - +
52A ASN 3.7 1.4 + - - -
53A PRO* 1.3 71.7 - - - +
55A LYS* 1.3 65.3 + - - +
130A HIS* 3.3 4.3 - - - -
131A VAL* 2.9 46.3 + - + +
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Residues in contact with LYS 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A PRO 4.4 4.0 - - - +
54A ALA* 1.3 77.3 - - - +
56A THR* 1.3 71.2 + - - +
58A GLU* 4.4 10.5 + - - +
128A THR* 4.0 16.9 + - + +
129A GLY 3.4 7.4 - - - +
130A HIS* 3.7 29.1 - - + +
201A GLU* 5.8 0.4 + - - -
230A GLU* 3.6 45.8 + - + +
281A TYR* 5.5 0.7 - - - -
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Residues in contact with THR 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A ALA* 3.9 0.4 + - + -
55A LYS* 1.3 86.8 - - - +
57A ARG* 1.3 69.3 + - - -
58A GLU* 4.9 1.0 - - - +
129A GLY 2.9 21.2 + - - -
131A VAL* 3.6 34.5 - - + -
198A VAL* 4.7 3.8 - - + +
217A ARG* 5.2 10.1 - - - +
220A PHE* 3.5 17.1 - - - -
221A ASN* 5.7 3.1 - - - -
229A HIS* 5.0 7.2 + - - -
230A GLU 4.7 9.7 + - - -
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Residues in contact with ARG 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A THR* 1.3 82.7 + - - +
58A GLU* 1.3 66.9 + - - +
59A TYR* 2.8 43.4 + - + -
128A THR* 3.9 0.9 - - - +
129A GLY 3.2 24.8 + - - -
220A PHE* 3.4 14.2 - - + -
221A ASN* 3.1 38.7 + - - +
223A LEU 5.2 0.8 + - - -
227A TRP* 3.8 50.0 - - + +
228A LYS 3.6 9.0 - - - +
229A HIS* 5.1 6.3 - - + +
240A ARG* 5.8 1.2 - - - +
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Residues in contact with GLU 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A LYS* 4.4 8.0 + - - -
56A THR 4.9 0.9 - - - +
57A ARG* 1.3 77.4 - - - +
59A TYR* 1.3 62.1 + - - +
126A LYS* 3.1 33.5 + - + +
127A ALA 3.6 5.2 - - - -
128A THR* 3.7 23.2 + - + +
227A TRP* 3.1 6.6 - - - +
228A LYS* 2.8 67.3 + - - +
230A GLU* 3.9 31.4 - - + +
235A TRP* 3.6 9.2 - - + -
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Residues in contact with TYR 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A ARG* 2.8 32.8 + - - -
58A GLU* 1.3 74.3 - - - +
60A CYS* 1.3 59.0 + - - +
126A LYS* 3.2 9.2 - - - +
127A ALA* 2.8 40.3 + - + +
220A PHE* 2.7 64.9 + + - -
221A ASN* 3.4 6.2 + - - -
223A LEU* 3.7 32.4 + - + -
225A LEU* 3.8 29.6 - - + -
226A PRO 3.2 14.1 - - - +
227A TRP* 3.5 19.7 - + + -
235A TRP* 3.6 4.0 - - - -
240A ARG* 5.1 0.2 - - - -
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Residues in contact with CYS 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A TYR* 1.3 73.4 - - - +
61A LEU* 1.3 60.6 + - - +
62A HIS 3.3 21.5 - - - -
63A ALA* 4.0 4.9 - - - -
120A ALA 4.4 1.8 - - - -
121A CYS* 2.0 51.4 - - + -
125A LYS 3.9 0.2 - - - -
225A LEU* 3.8 8.5 - - - +
226A PRO* 2.9 39.6 + - + +
235A TRP* 3.5 21.3 - - + -
241A LEU* 3.7 5.4 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il